Direct amplification and sequencing of enterovirus genomes from clinical and wastewater samples reveals uncommon virus types in Cameroon

Knowledge about the genetic diversity of enteroviruses in sub-Saharan Africa remains biased by the fact that it has mainly been described through the characterization of specimens isolated in cell cultures. The aim of this study was to characterize enteroviruses that circulate among humans in Cameroon by focusing more specifically on respiratory enteroviruses and on enteroviruses that are non-cultivable or non-cytopathogenic in standard cell lines. For this purpose, RNA was extracted from nasopharyngeal swabs, stool suspensions, and sewage concentrates collected in Cameroon from January 2018 to December 2019, and the RNA extracts were subjected to molecular screening to detect enterovirus genomes, which were subsequently sequenced using Illumina technology. Overall, 81 strains of 32 virus types were identified. Most of the strains (61.7%) belonged to the species Enterovirus coxsackiepol, followed by members of the species Enterovirus betacoxsackie (21%), Enterovirus alphacoxsackie (14.8%), and Enterovirus deconjuncti (2.5%). Almost all of the strains were found in sewage concentrates (79%) and stool suspensions (18.5%). Only two EV-D68 strains were identified in nasopharyngeal swabs. Interestingly, several virus types that have rarely been reported were detected, including non-cultivable/non-cytopathogenic EV-C strains, among which was a new virus type assigned as EV-C119. These results highlight the fact that virus isolation and unbiased cell-culture-free approaches complement each other to provide a more complete view of the enterovirus landscape in humans.